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r1261: code clean up; renamed --jump-bed to -j

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Also added --pairing to replace --no-pairing and --pe-ind-chain
This commit is contained in:
Heng Li
2025-04-06 18:32:58 -04:00
parent 3d351267a0
commit 38acd6617f
7 changed files with 53 additions and 50 deletions
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README.md
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@@ -20,8 +20,9 @@ cd minimap2 && make
./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam # spliced long reads (strand unknown)
./minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam # noisy Nanopore direct RNA-seq
./minimap2 -ax splice:hq -uf ref.fa query.fa > aln.sam # PacBio Kinnex/Iso-seq (RNA-seq)
./minimap2 -ax splice --junc-bed anno.bed12 ref.fa query.fa > aln.sam # use annotated junctions
./minimap2 -ax splice --junc-bed=anno.bed12 ref.fa query.fa > aln.sam # use annotated junctions
./minimap2 -ax splice:sr ref.fa r1.fq r2.fq > aln.sam # short-read RNA-seq (r1236+; experimental)
./minimap2 -ax splice:sr -j anno.bed12 ref.fa r1.fq r2.fq > aln.sam
./minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf # intra-species asm-to-asm alignment
./minimap2 -x ava-pb reads.fa reads.fa > overlaps.paf # PacBio read overlap
./minimap2 -x ava-ont reads.fa reads.fa > overlaps.paf # Nanopore read overlap
@@ -206,6 +207,10 @@ bonus score (tuned by `--junc-bonus`) if an aligned junction matches a junction
in the annotation. Option `--junc-bed` also takes 5-column BED, including the
strand field. In this case, each line indicates an oriented junction.
**Note:** that `--junc-bed` is intended for long noisy RNA-seq reads only.
Applying the option to short RNA-seq reads increase run time with little
improvement to junction accuracy.
#### <a name="long-overlap"></a>Find overlaps between long reads
```sh
@@ -234,8 +239,9 @@ mixed.
#### <a name="short-rna-seq"></a>Map short RNA-seq reads (experimental & evolving)
```sh
minimap2 -ax splice:sr ref.fa reads-se.fq > aln.sam # single-end
minimap2 -ax splice:sr ref.fa r1.fq r2.fq > aln.sam # paired-end
minimap2 -ax splice:sr ref.fa reads-se.fq.gz > aln.sam # single-end
minimap2 -ax splice:sr ref.fa r1.fq.gz r2.fq.gz > aln.sam # paired-end
minimap2 -ax splice:sr -j anno.bed ref.fa r1.fq r2.fq > aln.sam # use annotation
```
The new preset `splice:sr` was added between v2.28 and v2.29. It functions
similarly to `sr` except that it performs spliced alignment. Note that this